Discovery of new RNA virus species

RNA viruses are frequently studied in the context of disease, but they also offer valuable insights into RNA functionality. RNA is a versatile molecule that performs an exceptional set of cellular functions. Despite the many RNA functions and characteristics discovered over the past decades, new findings continue to emerge. To contribute to the understanding of RNA, we chose to study RNA viruses through observational research, as they are among the smallest operational units in nature in which RNA plays a dominant role. Viruses infect all sorts of life and display a remarkable array of strategies to enter their hosts and to propagate (International Committee on Taxonomy of Viruses, ICTV 2023). This is possible because RNA viruses have a high mutation rate which, combined with natural selection, allows for quick adaptation to changes in their host environment. These adaptations utilize the full capacity of known and unknown RNA functionalities. There is a saying: “Anything you can think of happening to RNA, there is a (plant) virus somewhere doing exactly that”. However, we believe that it should include, “and many things you would never think of.” Of course, the challenge remains to find RNA viruses with new characteristics and strategies that will elucidate or hypothesize yet unknown RNA functions. To optimize our chances for such discoveries, we turned to a group of host species where the knowledge about associated viruses is still limited, which is evolutionary distant from mammals and plants, that lives in an entirely different environment than terrestrial species, and is relatively easy to obtain: seaweed or macro-algae.

A contemporary approach to discovering (parts of) new non-pathogenic viruses involves large-scale metagenomics experiments that often analyze pooled samples from various sources. In our studies, rather than relying on these large-scale metagenomics experiments to discover and broadly describe as many variant or novel viruses as possible, typically based on RNA dependent RNA polymerase (RdRp) protein homology, we employ a more reductionistic approach (Dekker et al. 2024). Our goal is to discover the complete genomes of new RNA viruses, including hard-to-recognize segments, with a focus on capsidless viruses, using creative bioinformatics analyses to facilitate their discovery and delineate their genomic characteristics. By studying RNA viruses in seaweed, we aim to uncover novel RNA functionalities that could contribute to a better understanding of RNA biology.

Dekker RJ, de Leeuw WC, van Olst M, Ensink WA, van Leeuwen S, Cohen J, et al. Discovery of novel RNA viruses in commercially relevant seaweeds Alaria esculenta and Saccharina latissima. bioRxiv [Preprint]. 2024 May 22. doi: 10.1101/2024.05.22.594653. Available from: www.biorxiv.org/content/10.1101/2024.05.22.594653v1.

People working on this research line:

Dr. Martijs Jonker
M.J.Jonker at uva.nl
T 020-525-7939